Transcription of genes to the corresponding RNA molecules is a complex process which is catalyzed by DNA dependent RNA polymerase, and involves many different protein factors. In eubacteria, the core RNA polymerase is composed of α, β, and β′ subunits in the ratio 2:1:1. To direct RNA polymerase to promoters of specific genes to be transcribed, bacteria produce a variety of proteins, known as sigma (σ) factors, which interact with RNA polymerase to form an active holoenzyme. The resulting complexes are able to recognize and attach to selected nucleotide sequences in promoters.
Physical measurements have shown that the sigma subunit induces conformational transition upon binding to the core RNA polymerase. Binding of the sigma subunit to the core enzyme increases the binding constant of the core enzyme for DNA by several orders of magnitude (Chamberlin, M. J. (1974) Ann. Rev. Biochem. 43, 721-).
Characterisation of sigma subunits, identified and sequenced from various organisms, allows them to be classified into two broad categories; Group I and Group II. The Group I sigma has also been referred to as the sigma70 class, or the “house keeping” sigma group. Sigma subunits belonging to this group recognise similar promoter sequences in the cell. These properties are reflected in certain regions of the proteins which are highly conserved between species.
Bacterial sigma factors do not have any homology with eukaryotic transcription factors, and are consequently a potential target for antibacterial compounds. Mutations in the sigma subunit, affecting its association and ability to confer DNA sequence specificity to the enzyme, are known to be lethal to the cell.
Mycobacterium tuberculosis is a major pulmonary pathogen which is characterized by its very slow growth rate. As a pathogen it gains access to alveolar macrophages where it multiplies within the phagosome, finally lysing the cells and being disseminated through the blood stream, not only to other areas of the lung, but also to extrapulmonary tissues. Thus the pathogen multiplies in at least two entirely different environments, which would involve the utilisation of different nutrients and a variety of possible host factors; a successful infection would thus involve the coordinated expression of new sets of genes. This regulation would resemble different physiological stages, as best exemplified by Bacillus, in which the expression of genes specific for different stages are transcribed by RNA polymerases associating with different sigma factors. This provides the possibility of targeting not only the house keeping sigma of M. tuberculosis, but also sigma subunits specific for the different stages of infection and dissemination.